Biology subjects

Arribas, P.

Publications and source records attributed to Arribas, P..

5 recordsLinked to original sources

bioRxiv2026

Full-length COI barcodes improve eDNA metabarcoding data denoising relative to mini-barcodes

Animal COI (mitochondrial cytochrome oxidase I) metabarcoding of environmental DNA (eDNA) is increasingly used to assess biodiversity in complex substrates such as soil. However, due to read-length constraints of second-generation sequencing platforms, mini-barcodes have been used instead of the full barcode region. Long-read sequencing technologies now enable the recovery of full-length barcode sequences, and are more commonly applied for studying microbes, but their use for metabarcoding the full-length standard COI barcoding region in animals remains limited. In this study, we compared three COI amplicon sets - 313 bp, 660 bp, and 1,256 bp - amplified from soil eDNA samples and sequenced using Illumina and PacBio platforms to evaluate their overall concurrence, the effectiveness of identifying nuclear mitochondrial DNA segments (NUMTs) and chimeras, as well as their respective taxonomic resolution. The long-read datasets exhibited a higher identification rate of NUMTs and true chimeras, suggesting that longer sequences improve the detection of noise in COI metabarcoding data, thereby reducing the occurrence of spurious taxa. Taxonomy assignment confidence was similar between the 313 bp and 660 bp datasets, whereas extending the amplicon beyond the standard COI barcode region (1,256 bp) reduced confidence, likely because longer reads extend into regions poorly represented in barcode reference databases. Despite substantially lower sequencing depth in the 660 bp dataset, per-sample OTU richness did not differ significantly from that recovered with the Illumina 313 bp amplicon set. Similarly, the relationships between samples were strongly correlated across the detected OTU communities, indicating consistent ecological interpretations between short and long amplicons. We conclude that the standard [~]658 bp COI barcode is an optimal marker for soil animal metabarcoding from eDNA, balancing target recovery, artifact detection, taxonomic assignment and ecological interpretability. As COI eDNA metabarcoding becomes increasingly used in biodiversity assessment and is increasingly adopted in large-scale monitoring initiatives, this study provides methodological guidance for improving the robustness of soil animal community biomonitoring.

ecology↗

bioRxiv2020

The limited spatial scale of dispersal in soil arthropods revealed with whole-community haplotype-level metabarcoding

Soil mesofauna communities are hyperdiverse and critical for ecosystem functioning. However, our knowledge on spatial structure and underlying processes of community assembly for soil arthropods is scarce, hampered by limited empirical data on species diversity and turnover. We implement a high-throughput-sequencing approach to generate comparative data for thousands of arthropods at three hierarchical levels: genetic, species and supra-specific lineages. A joint analysis of the spatial arrangement across these levels can reveal the predominant processes driving the variation in biological assemblages at the local scale. This multi-hierarchical approach was performed using haplotype-level-COI metabarcoding of entire communities of mites, springtails and beetles from three Iberian mountain regions. Tens of thousands of specimens were extracted from deep and superficial soil layers and produced comparative phylogeographic data for >1000 co-distributed species and nearly 3000 haplotypes. Local assemblages were highly distinctive between grasslands and forests, and within each of them showed strong spatial structures and high endemicity at the scale of a few kilometres or less. The local distance-decay patterns were self-similar for the haplotypes and higher hierarchical entities, and this fractal structure was very similar in all three regions, pointing to a significant role of dispersal limitation driving the local-scale community assembly. Our results from whole-community metabarcoding provide unprecedented insight into how dispersal limitations constrain mesofauna community structure within local spatial settings over evolutionary timescales. If generalized across wider areas, the high turnover and endemicity in the soil locally may indicate extremely high richness globally, challenging our current estimations of total arthropod-diversity on Earth.

ecology↗

bioRxiv2020

NUMT dumping: validated removal of nuclear pseudogenes from mitochondrial metabarcode data

Metabarcoding of Metazoa using mitochondrial genes may be confounded by both the accumulation of PCR and sequencing artefacts and the co-amplification of nuclear mitochondrial pseudogenes (NUMTs). The application of read abundance thresholds and denoising methods is efficient in reducing noise accompanying authentic mitochondrial amplicon sequence variants (ASVs). However, these procedures do not fully account for the complex nature of concomitant sequences and the highly variable DNA contribution of individuals in a metabarcoding sample. We propose, as a complement to denoising, the metabarcoding Multidimensional Abundance Threshold Evaluation (metaMATE) framework, a novel approach that allows comprehensive examination of multiple dimensions of abundance filtering and the evaluation of the prevalence of unwanted concomitant sequences in denoised metabarcoding datasets. metaMATE requires a denoised set of ASVs as input, and designates a subset of ASVs as being either authentic (mtDNA haplotypes) or non-authentic ASVs (NUMTs and erroneous sequences) by comparison to external reference data and by analysing nucleotide substitution patterns. metaMATE (i) facilitates the application of read abundance filtering strategies, which are structured with regard to sequence library and phylogeny and applied for a range of increasing abundance threshold values, and (ii) evaluates their performance by quantifying the prevalence of non-authentic ASVs and the collateral effects on the removal of authentic ASVs. The output from metaMATE facilitates decision-making about required filtering stringency and can be used to improve the reliability of intraspecific genetic information derived from metabarcode data. The framework is implemented in the metaMATE software, available at https://github.com/tjcreedy/metamate).

evolutionary biology↗

bioRxiv2019

A validated workflow for rapid taxonomic assignment and monitoring of a national fauna of bees (Apiformes) using high throughput barcoding

Improved taxonomic methods are needed to quantify declining populations of insect pollinators. This study devises a high-throughput DNA barcoding protocol for a regional fauna (United Kingdom) of bees (Apiformes), consisting of reference library construction, a proof-of-concept monitoring scheme, and the deep barcoding of individuals to assess potential artefacts and organismal associations. A reference database of Cytochrome Oxidase subunit 1 (cox1) sequences including 92.4% of 278 bee species known from the UK showed high congruence with morphological taxon concepts, but molecular species delimitations resulted in numerous split and (fewer) lumped entities within the Linnaean species. Double tagging permitted deep illumina sequencing of 762 separate individuals of bees from a UK-wide survey. Extracting the target barcode from the amplicon mix required a new protocol employing read abundance and phylogenetic position, which revealed 180 molecular entities of Apiformes identifiable to species. An additional 72 entities were ascribed to mitochondrial pseudogenes based on patterns of read abundance and phylogenetic relatedness to the reference set. Clustering of reads revealed a range of secondary Operational Taxonomic Units (OTUs) in almost all samples, resulting from traces of insect species caught in the same traps, organisms associated with the insects including a known mite parasite of bees, and the common detection of human DNA, besides evidence for low-level cross-contamination in pan traps and laboratory steps. Custom scripts were generated to conduct critical steps of the bioinformatics protocol. The resources built here will greatly aid DNA-based monitoring to inform management and conservation policies for the protection of pollinators.

molecular biology↗

bioRxiv2018

The contribution of mitochondrial metagenomics to largescale data mining and phylogenetic analysis of Coleoptera

A phylogenetic tree at the species level is still far off for highly diverse insect orders, including the Coleoptera, but the taxonomic breadth of public sequence databases is growing. In addition, new types of data may contribute to increasing taxon coverage, such as metagenomic shotgun sequencing for assembly of mitogenomes from bulk specimen samples. The current study explores the application of these techniques for large-scale efforts to build the tree of Coleoptera. We used shotgun data from 17 different ecological and taxonomic datasets (5 unpublished) to assemble a total of 1942 mitogenome contigs of >3000 bp. These sequences were combined into a single dataset together with all mitochondrial data available at GenBank, in addition to nuclear markers widely used in molecular phylogenetics. The resulting matrix of nearly 16000 species with two or more loci produced trees (RAxML) showing overall congruence with the Linnaean taxonomy at hierarchical levels from suborders to genera. We tested the role of full-length mitogenomes in stabilizing the tree from GenBank data, as mitogenomes might link terminals with non-overlapping gene representation. However, the mitogenome data were only partly useful in this respect, presumably because of the purely automated approach to assembly and gene delimitation, but improvements in future may be possible by using multiple assemblers and manual curation. In conclusion, the combination of data mining and metagenomic sequencing of bulk samples provided the largest phylogenetic tree of Coleoptera to date, which represents a summary of existing phylogenetic knowledge and a defensible tree of great utility, in particular for studies at the intra-familial level, despite some shortcomings for resolving basal nodes.

evolutionary biology↗